The Dark Ocean Biosphere

The Dark Ocean Biosphere exists in a different energy dynamic than what we know from our own sunlit lives and it is encountered using robots and submersibles like JAGO (research theme photo)  or Doc Ricketts (Fig. 1 and Fig. 2).  The deep sea consists of microbial environments in the aphotic pelagic water column and in sediments, pore waters, hydrothermal vents and the upper basaltic crust. Depending on the quantity of particulate matter in the water, levels of sunlight sufficiently high to enable  photosynthesis penetrate only a few tens to hundreds of meters  into the  ocean. In the mesopelagic “twilight zone” (200m – 1000 m) and completely dark realms of the bathypelagic water layers (1000m – 4000 m) the sources for organic material fueling the metabolism of deep oceanic microbes are not obvious – allowing for exciting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles!

In OEB we examine microbes involved in organic matter cycling and biogeochemistry in the ocean, especially of the elements carbon, nitrogen, sulfur and non-protein organic compounds like vitamins. We also study multicellular eukaryotic animals, like corals (Fig. 3, 4) and zooplankton! We aim to understand the structure and dynamics of natural microbial communities – from the single cell level to organismal interactions and communities, including microbiomes, — that collectively comprise the biota of these dark environments.

We combine laboratory experiments and analyses with ship-going research. For microbial research some studies focus on genomic, transcriptomic, and proteomic technologies, single cell analyses (CARD-FISH, Click-chemistry) and mass spectrometry to describe and explore the genomics, biochemistry, metabolism and ecology of marine Bacteria and Archaea – and their effects on global ecosystem processes (e.g., Bergauer et al. PNAS 2018; Pachiadaki et al. Science 2017; Sintes et al. Environ. Microbiol. 2013). This latter research is being led by  Kristin Bergauer.

Other OEB research under this theme is led by Helena Hauss and Alexandra Worden. This research adds to water column work by looking at the activities of deep sea microbes using our newly developed Deep Sea Sediment Injector (DSSI) samplers (Fig. 5) and Bird Bag Incubators (Fig. 4).

With these, Dr. Rachel Harbeitner (who completed her PhD in the Worden Lab and a mini-postdoc) is studying microbial community structure and connectivity throughout the water column and sediments (Fig. 6) and Dr. Sebastian Sudek is working on microbial activities in the sediments.

Our PhD student Charlotte Eckmann is studying the microbiome associated with deep-sea corals (Fig. 3 and Fig. 7), providing structural habitats that are considered biodiversity hotspots. Victoria Orphan (CalTech) often joins in with us for these experiments. Our DSSI samplers are also being used by the Orphan/Goffredi, A. Dekas (Stanford University) and T. Richards (Oxford University) Labs. Our first paper on them is Rodríguez-Martínez et al. ISME J 2020. Further, we examine multicellular organisms that thrive in this biosphere – many of which also migrate into surface waters on short time scales.

Connections to OEB Pelagic Processes & Food Webs theme.